Function reference
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allocateCells() - Annotate all cells with contour level of cell type-specific density.
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cellsInRegion() - Check which cells are in which regions
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computeDensity() - Perform kernel density estimation on SpatialExperiment
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contour2sf() - Draw a contour region on some density level
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corDensity() - Test for density correlation between two cell types.
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findROI() - Find ROIs based on cell type-specific densities via graph-based method.
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getContour() - Get contour from density
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getContourRegions() - Calculate areas between every two density levels
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grid2sf() - Combine grids in each ROI to a sf region
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gridDensity() - Perform kernel density estimation on SpatialExperiment for cell types of interest
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mergeROI() - Manually merge ROIs
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plotCellCompo() - Plot cell type composition in each density level of cell of interest.
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plotContour() - Plot contour lines.
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plotContourRegion() - Visualising an sf object (for internal use only at the moment)
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plotCorHeatmap() - Plot model statistics using heatmap.
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plotDensCor() - Plot density correlation between two cell types
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plotDensity() - Plot grid-based density.
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plotROI() - Plot ROIs on spatial.
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plotSpatial() - Plot cells based on spatial coordinates.
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postSelRegion() - Merge sel_region from the selectRegion function to SpatialExperiment.
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selectRegion() - Select region of interest from plot
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spe2PB() - Given a 'SpatialExperiment' data object, create pseudo-bulk samples using the colData information and return a DGEList object